diff emboss_wordmatch.xml @ 10:9b98d3d903c6 draft

planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/emboss_5 commit fc158bfe5f5927dc199321a2cf43310373cbc8ba

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/emboss_wordmatch.xml	Fri Aug 12 19:17:10 2016 -0400
@@ -0,0 +1,82 @@
+<tool id="EMBOSS: wordmatch110" name="wordmatch" version="5.0.0">
+  <description>Finds all exact matches of a given size between 2 sequences</description>
+  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
+  <command>wordmatch -asequence $input1 -bsequence $input2 -outfile $out_file1 -aoutfeat $out_file2 -boutfeat $out_file3 -wordsize "$wordsize" -aformat3 $out_format1 -offormat4 $out_format2
+  -offormat5 $out_format3 -auto</command>
+  <inputs>
+    <param format="fasta" name="input1" type="data">
+      <label>Sequence 1</label>
+    </param>
+    <param format="fasta" name="input2" type="data">
+      <label>Sequence 2</label>
+    </param>
+    <param name="wordsize" type="text" value="4">
+      <label>Word size</label>
+    </param>
+    <param name="out_format1" type="select">
+      <label>Output Alignment File Format</label>
+      <option value="match">Match (m)</option>
+      <option value="simple">Simple (m)</option>
+      <option value="fasta">FASTA (m)</option>
+      <option value="msf">MSF (m)</option>
+      <option value="srs">SRS (m)</option>
+      <option value="pair">Pair (p)</option>
+      <option value="markx0">Markx0 (p)</option>
+      <option value="markx1">Markx1 (p)</option>
+      <option value="markx2">Markx2 (p)</option>
+      <option value="markx3">Markx3 (p)</option>
+      <option value="markx10">Markx10 (p)</option>
+      <option value="srspair">SRS pair (p)</option>
+      <option value="score">Score (p)</option>
+    </param>
+    <param name="out_format2" type="select">
+      <label>Output Feature 1 File Format</label>
+      <option value="gff">GFF</option>
+      <option value="embl">EMBL</option>
+      <option value="swiss">SwissProt</option>
+    </param>
+    <param name="out_format3" type="select">
+      <label>Output Feature 2 File Format</label>
+      <option value="gff">GFF</option>
+      <option value="embl">EMBL</option>
+      <option value="swiss">SwissProt</option>
+    </param>
+  </inputs>
+  <outputs>
+    <data format="match" name="out_file1" />
+    <data format="gff" name="out_file2" />
+    <data format="gff" name="out_file3" />
+  </outputs>
+  <!--   <tests>
+    <test>
+      <param name="input1" value="2.fasta"/>
+      <param name="input2" value="1.fasta"/>
+      <param name="wordsize" value="4"/>
+      <param name="out_format1" value="fasta"/>
+      <param name="out_format2" value="gff"/>
+      <param name="out_format3" value="gff"/>
+      <output name="ofile2" file="emboss_wordmatch_out.embl"/>
+    </test> 
+  </tests> test takes a long time to run-->
+  <code file="emboss_format_corrector.py" />
+  <help>
+
+.. class:: warningmark 
+
+The input datasets need to be sequences. 
+
+----- 
+
+    You can view the original documentation here_.
+    
+    .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/wordmatch.html
+
+------
+
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. &lt;http://www.ncbi.nlm.nih.gov/pubmed/10827456&gt;`_
+
+If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. &lt;http://www.ncbi.nlm.nih.gov/pubmed/17568012&gt;`_
+  </help>
+</tool>